[gmx-users] Interactions between tow chains of a protein

Polavarapu, Abhigna polavara at indiana.edu
Thu Nov 6 16:50:26 CET 2008

 Hi All,
         I am abhigna. I wanted to simulate a protein which binds to
Copper. Copper interacts with amino acids of Chain A and B of the
Dimeric protein. When I convert the pdb file to topology file this is
how it defines with A and B with protein and C and D with Copper. So I
need to define a bond between Copper and amino acids in chain A and B.
So How can I do that as I need to define the force field for copper in
the .top file.

[ molecules ]
; Compound        #mols
Protein_A           1
Protein_C           1
Protein_B           1
Protein_D           1
SOL                20
SOL                20

Thank you

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